Abstract: As an ectotherm, fish are highly susceptible to changes in temperature, which can have a significant impact on their reproductive cycles. In this study, we examined the fertility and histological characteristics of zebrafish (Danio rerio) ovaries exposed to a temperature gradient from the species' thermopreferendum temperature of 27°C to low temperatures of 22°C, 20°C, and 13°C for two weeks. Comparative analyses of metabolomics (six biological replicates for each temperature) and transcriptomics (four biological replicates for each temperature) were conducted under the four distinct temperature conditions. We found low temperatures inhibited the development of oocyte and from which identified differential metabolites involved in steroid hormone production, antioxidant function, and catabolism of lipid and protein. The disrupted reproductive hormones, increased proteolysis and lipid degradation greatly halted oocyte development and egg maturation. More interestingly, we found a significant increase in bile acids content in the ovary of the cold treated fish, and proved the bile acids constitute a significant contributing factor to ovarian failure. Our findings offer valuable insights into the mechanisms governing the response of fish reproduction to cold stress.